MOLECULAR DYNAMICS SIMULATIONS & METHOD DEVELOPMENT: DRUG DESIGN

分子动力学模拟

• 批准号: 6456689
• 负责人: PIOTR CIEPLAK
• 金额: $ 27.32万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-07-01 至 2003-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6456689
• 关键词: biological products; biomedical resource; computers; nucleic acids; proteins

We use the Computer Graphics Laboratory facilities to display and analyze the molecular dynamics simulations results. Our research projects focus on a) refining, testing and developing the new generation of additive and nonadditive force field parameters; and b) macromolecular simulation using molecular dynamics. The new approach, based on continuum solvent analysis, has been applied to analyze molecular dynamics trajectories. This new approach provides direct free energies of the solute in the aqueous solution with remarkable accuracy. We have applied this method to analyze trajectories of dodecamer duplex d(CGCGAATTCGCG)2 and its phosphoramidate (N-P) analog in water solution. The continuum solvent analysis quantitatively described the preference of the normal DNA to exist predominately in B form in water solution, whereas the 3' phosphoramidate modified DNA duplex in the A form. This work is undergoing further development of the additive and nonadditive AMBER force field. The nonadditive AMBER parametrization includes nonadditive effects based on atomic polarizabilities and lone pairs interactions.

我们使用计算机图形实验室的设施来显示和